cibrrig.gui

Attributes

brain_xyz_path
ba
DEFAULT_SUBJECTS_PATH
DEFAULT_ARCHIVE_PATH
DEFAULT_WORKING_PATH
OCCIPITAL_APEX
OCCIPITAL_NADIR
LAMBDA_IBL
PITCH_CORRECTION
COLORS
INSERTION_TYPES
DEFAULT_WIRING
POSSIBLE_WIRINGS

Classes

DirectorySelector	GUI to select paths for backup. Expands QWidget.
OptoFileFinder	Dialog box to select the opto_calibration.json file if it is not found
WiringEditor	Dialog box to select the wiring file
InsertionTableAppBase
NpxInsertionTableApp
OptoInsertionTableApp
NotesDialog

Functions

get_tip(x, y, z, d, phi, theta)	Ripped from iblatlas because we don't want to use the
insertion2IBL(df)	Convert insertion coordinates to IBL coordinates
convert2ccf(df)	Convert IBL coordinates to CCF coordinates
plot_probe_insertion(df, save_fn)
plot_probe_insertion_urchin(df, save_fn)
plot_probe_insertion_ibl(df, save_fn)
plot_insertion_layout(df, save_fn)

Module Contents

cibrrig.gui.brain_xyz_path

cibrrig.gui.ba

cibrrig.gui.DEFAULT_SUBJECTS_PATH

cibrrig.gui.DEFAULT_ARCHIVE_PATH

cibrrig.gui.DEFAULT_WORKING_PATH

cibrrig.gui.OCCIPITAL_APEX

cibrrig.gui.OCCIPITAL_NADIR

cibrrig.gui.LAMBDA_IBL

cibrrig.gui.PITCH_CORRECTION = 0

cibrrig.gui.COLORS = ['#ff0000', '#00ff00', '#0000ff', '#ffff00', '#ff00ff', '#00ffff', '#ff8000', '#ff0080',...

cibrrig.gui.INSERTION_TYPES = ['npx1.0', 'npx2.0', 'opto_200um', 'opto_400um', 'opto_600um']

cibrrig.gui.DEFAULT_WIRING

cibrrig.gui.POSSIBLE_WIRINGS

cibrrig.gui.get_tip(x, y, z, d, phi, theta)

Ripped from iblatlas because we don’t want to use the the atlas nor assume that the probe insertion point should be at the brain

cibrrig.gui.insertion2IBL(df)

Convert insertion coordinates to IBL coordinates dataframe must have the following columns: - Insertion ML (microns) - Insertion AP (microns) - Insertion DV (microns) - Reference (“occipital apex”, “occipital nadir”, “lambda”, “bregma”)

Parameters:

df (pd.DataFrame) – DataFrame with insertion coordinates

Returns:

DataFrame with IBL coordinates

Return type:

pd.DataFrame

cibrrig.gui.convert2ccf(df)

Convert IBL coordinates to CCF coordinates

In IBL frame, bregma is at (0,0,0) and right is positive x, rostral is positive y, dorsal is positive z x,y,z -> ML, AP, DV

In CCF frame, bregma is at (5400, 5739, 332) (AP,ML,DV) and right is positive x, caudal is positive y, ventral is positive z

dataframe must have the following columns: - x - y - z - phi (azimuth/yaw) - theta (pitch/elevation) - Depth (microns)

Parameters:

df (pd.DataFrame) – DataFrame with IBL coordinates

Returns:

DataFrame with CCF coordinates

Return type:

pd.DataFrame

cibrrig.gui.plot_probe_insertion(df, save_fn)

async cibrrig.gui.plot_probe_insertion_urchin(df, save_fn)

cibrrig.gui.plot_probe_insertion_ibl(df, save_fn)

cibrrig.gui.plot_insertion_layout(df, save_fn)

class cibrrig.gui.DirectorySelector

Bases: PyQt5.QtWidgets.QWidget

GUI to select paths for backup. Expands QWidget.

This class provides a graphical user interface (GUI) for selecting local and remote paths for backup, as well as options for removing optogenetic artifacts and running ephys quality control.

local_run_path

Path to the local run directory.

Type:

Path

remote_archive_path

Path to the remote archive directory.

Type:

Path

remote_working_path

Path to the remote working directory.

Type:

Path

remove_opto_artifact

Option to remove optogenetic artifacts.

Type:

bool

run_ephys_qc

Option to run ephys quality

Type:

bool

Parameters:

QWidget (QWidget) – Base class QWidget.

local_run_path

remote_archive_path

remote_working_path

remove_opto_artifact = False

run_ephys_qc = True

init_ui()

Initialize the UI layout.

select_local_run_path()

Select the local run path with UI

select_remote_archive_path()

Select the remote archive path with UI

select_remote_working_path()

Select the remote working path with UI

toggle_remove_opto_artifact(state)

Toggle the remove_opto_artifact checkbox

get_gates()

infer_num_probes()

get_session_info()

submit()

get_paths()

Return the selected paths and options

class cibrrig.gui.OptoFileFinder(title='')

Bases: PyQt5.QtWidgets.QDialog

Dialog box to select the opto_calibration.json file if it is not found

opto_file

Path to the opto_calibration.json file

Type:

Path

opto_file_selected

select_button

opto_file = None

select_file()

Select the opto_calibration.json file with UI

skip_file()

Skip the opto_calibration.json file

get_opto_file()

class cibrrig.gui.WiringEditor(title='')

Bases: PyQt5.QtWidgets.QDialog

Dialog box to select the wiring file

output_wiring

Dictionary of the selected wiring

Type:

dict

digital_entries

Dictionary of the digital mapping (channels: signals)

Type:

dict

analog_entries

Dictionary of the analog mapping (channels: signals)

Type:

dict

title = ''

initUI()

Initialize the UI layout

on_digital_value_changed(combo_box, key)

Update the digital value

on_analog_value_changed(combo_box, key)

Update the analog value

save_values()

Save the output wiring attributes

get_output_wiring()

class cibrrig.gui.InsertionTableAppBase(n_rows=1, n_gates=20, name='', save_fn=None)

Bases: PyQt5.QtWidgets.QDialog

n_gates = 20

save_fn = None

name = ''

df = None

table

get_headers()

add_row(row)

get_insertion_types()

update_angles(row)

add_new_row()

delete_last_row()

copy_previous_row(current_row_count)

add_new_column()

export_to_dataframe()

convert_and_export()

create_dataframe()

get_insertions()

to_csv()

load_csv()

Load a csv and populate the table if it exists

populate_table()

Populate the table with data from a dataframe

class cibrrig.gui.NpxInsertionTableApp(n_rows=1, n_gates=10, name='', save_fn=None)

Bases: InsertionTableAppBase

get_insertion_types()

add_row(row)

convert_and_export()

class cibrrig.gui.OptoInsertionTableApp(n_rows=1, n_gates=10, name='', save_fn=None)

Bases: InsertionTableAppBase

get_headers()

get_insertion_types()

add_row(row)

convert_and_export()

class cibrrig.gui.NotesDialog(n_gates, notes_fn)

Bases: PyQt5.QtWidgets.QDialog

notes_fn

overall_notes_text

text_fields = []

submit()

save_notes()

load_notes()